Contacts of the strand formed by residues 1156 - 1163 (chain A) in PDB entry 1AWV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE1156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A ILE* 3.9 15.5 - - + -
1011A ALA 3.5 2.2 - - - +
1012A VAL* 4.2 15.9 - - + -
1052A CYS* 3.0 7.0 - - - +
1053A PHE* 3.0 48.1 + - + +
1056A ILE* 3.6 20.6 - - + -
1142A MET* 3.6 34.1 - - + +
1145A PHE* 3.5 39.5 - - + +
1152A THR* 4.4 3.3 + - + +
1154A LYS 3.4 8.4 + - - +
1155A LYS* 1.3 76.0 - - - +
1157A THR* 1.3 59.8 + - - +
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Residues in contact with THR1157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A ILE* 3.4 10.1 - - - +
1011A ALA* 2.9 41.1 + - - -
1013A ASP 5.1 1.6 + - - -
1014A GLY* 5.1 3.8 + - - -
1050A GLY* 3.3 29.2 - - - +
1051A SER 3.5 5.2 - - - +
1053A PHE* 5.2 0.7 - - - -
1155A LYS* 3.2 34.6 + - - +
1156A ILE* 1.3 74.9 - - - +
1158A ILE* 1.3 78.2 + - - +
1159A ALA* 3.2 4.6 + - - +
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Residues in contact with ILE1158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A PHE* 3.8 31.0 - - + -
1009A ASP 3.7 2.9 - - - -
1010A ILE* 4.3 6.3 - - + -
1048A TYR* 3.4 40.2 - - + +
1049A LYS* 3.7 0.2 - - - -
1050A GLY* 2.8 25.3 + - - -
1051A SER* 2.9 24.6 + - - +
1052A CYS 5.6 0.9 - - - +
1053A PHE* 3.7 25.4 - - + -
1065A GLY 5.7 0.4 - - - +
1112A PHE* 4.6 4.3 - - + -
1157A THR* 1.3 70.0 - - - +
1159A ALA* 1.3 61.7 + - - +
1160A ASP 3.9 11.2 - - - +
1161A CYS* 3.8 22.9 - - - -
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Residues in contact with ALA1159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A ASP* 2.6 24.1 + - + +
1010A ILE 4.6 0.7 - - - -
1011A ALA* 3.8 23.6 - - + -
1014A GLY 5.8 0.2 - - - +
1016A PRO* 5.9 3.8 - - + -
1049A LYS* 3.3 21.7 - - - +
1050A GLY* 4.9 0.8 + - - -
1157A THR* 3.2 8.5 + - - -
1158A ILE* 1.3 73.6 - - - +
1160A ASP* 1.3 57.3 + - + +
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Residues in contact with ASP1160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007A PHE* 5.4 2.7 - - - -
1008A PHE* 3.2 2.1 - - - -
1009A ASP* 2.4 58.9 + - + +
1049A LYS* 3.5 29.5 + - - +
1158A ILE* 3.2 2.7 - - - +
1159A ALA* 1.3 81.0 - - + +
1161A CYS* 1.3 73.2 + - - +
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Residues in contact with CYS1161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007A PHE* 2.9 32.1 - - - +
1008A PHE* 3.3 15.7 - - + -
1040A SER 3.1 29.5 - - - +
1041A THR* 4.8 2.4 - - - +
1048A TYR* 3.9 6.3 - - - -
1049A LYS* 3.2 43.7 - - - +
1158A ILE* 3.8 5.6 - - + -
1160A ASP* 1.3 83.2 + - - +
1162A GLY* 1.3 56.9 + - - +
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Residues in contact with GLY1162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006A VAL* 3.2 5.5 - - - -
1007A PHE* 2.9 48.6 + - - -
1040A SER* 3.2 14.1 + - - -
1041A THR* 4.4 5.8 - - - -
1161A CYS* 1.3 77.7 - - - +
1163A GLN* 1.3 58.7 + - - -
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Residues in contact with GLN1163 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A PRO* 3.8 10.7 - - - +
1005A THR 3.4 8.5 - - - +
1006A VAL* 4.0 8.1 - - + -
1037A ARG* 3.1 44.1 + - - +
1041A THR* 3.8 19.8 - - + +
1162A GLY* 1.3 71.5 - - - -
1164A LEU* 1.3 66.1 + - - +
1165A GLU* 2.9 34.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il